The invention relates to the field of geophysical exploration equipment and particularly relates to a magnetic resonance water detection system and method for increasing the amplitude of an acquired signal. The system includes a transmitter which includes a first main controller and is used for controlling a first storage battery for charging a first energy storage capacitor for providing heavy current transmission energy for a transmitting coil, a compensation device which includes a second main controller and is used for controlling a second storage battery for charging a second energy storage capacitor for providing transmission energy for a compensation coil, a receiving device which includes an AD acquisition card and is used for transmitting a synchronous signal through the second main controller for MRS signal or coupling signal acquisition, and a PC host computer, wherein excitation pulses are generated through the compensation coil, coupling generated by transmission pulses ina receiving coil is offset, and a charging signal and a transmission AC pulse control signal are transmitted to the first main controller. The system is advantaged in that the compensation coil is utilized to offset an induced signal generated through coupling in the receiving coil when the transmitting coil is emitted, and a problem of loss of an effective signal caused by the dead area time iseffectively solved.